您好，欢迎访问贵州省农业科学院 机构知识库！
贵州省农业科学院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.)

文献类型： 外文期刊

作者： Li, Yadong 1 ; Luo, Xiaobo 3 ; Peng, Xiao 1 ; Jin, Yueyue 1 ; Tan, Huping 1 ; Wu, Linjun 1 ; Li, Jingwei 1 ; Pei, Yun 1 ; Xu, Xiuhong 1 ; Zhang, Wanping 1 ;

作者机构： 1.Guizhou Univ, Coll Agr, Guiyang 550003, Peoples R China

2.Guizhou Univ, Inst Vegetable Ind Technol Res, Guiyang 550003, Peoples R China

3.Guizhou Prov Acad Agr Sci, Guizhou Inst Biotechnol, Guiyang 550003, Peoples R China

关键词： Radish; InDel; Genetic diversity; Population structure; Transcriptome; Flowering

期刊名称：BMC GENOMICS （ 影响因子：4.4； 五年影响因子：4.7 ）

ISSN： 1471-2164

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundSingle nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.).ResultsIn this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained.ConclusionsThe large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.

  • 相关文献
作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：贵州省农业科学院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台